The isolation of single types of chromosomes is a critical technology for a wide variety of research projects. These projects include genetics, cell biology, human genome program, and cancer biology. The challenge is to recover large numbers of chromosomes with high purity and high molecular weight in a relatively short period of time. Our approach has been to develop an optical sorter for high speed sorting and to adapt commercial sorters (EPICS V and EPICS 752) for conventional chromosome sorting. All three units have dual laser excitation for Chromomycin A3 and Hoechst 33258 bound to the chromosomes. The optical sorter will be capable of sorting rates approximately 50 times faster than the commercial sorters. With the recent success of cloning very large pieces of DNA(>100 kb) into a variety of large insert cloning vectors, the need for high throughput has become crucial. We have validated the technique of optical sorting by demonstrating the cross-linking and subsequent elimination of colony growth of 99% of the unwanted colonies. This success has been achieved using new cross-linking compounds which do not absorb in the region of the chromomycin and Hoechst molecules. The results of the experiments clearly indicate that these cross-linking agents can, when exposed to UV light, eliminate the ability of the exposed chromosomes to be cloned into cosmid vectors.